well, now i get to join this thread, but my story might be a little different.
right after i filed, i got a notice saying the full amount of my refund had been held back, but when i investigated my bank account, i was only short a very small amount corresponding to the foreign tax credit i had. that was months and months ago. now i cant even remember if that was resolved - the amount was so small i just didn't care.
on saturday i received a huge package from the IRS - form 4549, "income tax examination changes." unfortunately the explanation was at the end and i missed it, which caused some stress. anyway the math on the form says that i have underpaid my taxes by $7500 and i'm being levied a $1500 fine for underpayment. i called them this morning and the person i talked to alerted me to the explanation form at the very end of the stack... that form says they want proof that i own the car - sales contract and registration. i have no idea if turning that in that will solve the problem, but i hope so.
i've heard that if you ask nicely and explain that there was no intent to defraud, that they will waive the fines. i don't expect to need to do this, because it seems to me that there's no reason why the credit should be rejected based on other peoples' resolution of the problem in this thread.